I had an email exchange with Jeff Johannes at Astra-Zeneca back in Feb 2013 on using methanol for flash columns. We agreed that it was worth posting on a noticeboard, so I post it here now.Jeff:Thanks for these emails (solvent of the week), I have been enjoying them each week. I would like to ask you about this statement:“Methanol can be added to solvents for flash chromatography but don't use more than 10% or it will start to dissolve the silica.”Is it really true? I used to think this in grad. school, but since moving to a job in the pharmaceutical industry for the last 6 years we routinely run 20 or even 30% MeOH in DCM to purify really polar compounds without accumulating silicon dioxide in our samples. Is there a published paper on the solubility of silica in MeOH?

Matthew:Hi Jeff, Thanks for your thoughts and it's a very good question. :)I have not come across any peer reviewed papers on the matter. I base my comment of not exceeding 10% MeOH on flash columns on general views. I like to keep solvent of the week short so that it appeals to a wide audience and does not take up too much of people's day.

I think you are right that there are many exceptions to the 10% rule

Dissolve is really the wrong word as silica is not really what we would call "miscible" in MeOH. I've tried to gloss over this by saying "start to dissolve" to avoid opening the can of worms in the short solvent of the week email

My more senior colleague with the most flash column experience in our group tells me that any more than 10% MeOH and he gets amorphous white solids in his test tubes. I believe this happens readily but not because the silica was miscible and crashed out on the other side but because some grades of silica have a more broad particle size distribution than others and possibly more than the pack specifies. MeOH has a way of loosening the smallest particles from the packing and bringing them down to the frit where if they are small enough and under pressure they can pass through. Another description is that MeOH disturbs the silica into a thixotropic gel-like solution with poor particulate separation.

I believe you are on to something about getting away with a higher percent MeOH in chlorinated solvents like DCM/chloroform. Depending on the compounds present MeOH can become slightly acidic which allows the smallest most amorphous parts of the silica to pass into solution for the briefest of moments and I reckon the DCM stabilizes MeOH a bit against becoming acidic.

A higher grade of consistent particle size silica is probably less prone to this effect (at Universities we use cheap, old or reactivated shit).

I have certainly tried TLCs in 20% MeOH and I find that it disturbs the silica away from the aluminium plate, rendering the TLC unreadable. This of course is different to a packed column.

Opinions on this matter are often passed down in a haphazard way. It is very useful of you to point out to our group your experience of using 20 or 30% MeOH in DCM for columns. Can you tell us what sort of compounds this has worked with?

We are also curious of your preferred method of deactivating silica for sticky compounds? We often use formic acid or triethylamine.

Jeff:Hi Matthew, thanks for writing back. One big difference that typically exists between academic and big pharma labs is that we exclusively use ISCO chromatography systems, which includes the ISCO columns which are pre-packed in a plastic cartridge and generally pretty good quality. The silica gel in these pre-packed columns is pretty good and they have good frits. So the combination of higher quality silica and better frits may greatly reduce the amount of silica that comes through. When I was in grad school it was just a cotton plug and sand holding back that silica gel!The DCM-MeOH is quite common for purifying really polar heterocycles (usually with unprotected NH or OH groups) or really basic amines. For really sticky basic amines, a very small percentage of concentrated NH4OH in H2O can be added to the DCM-MeOH system. Sticky acids are less common (we don’t make a lot of acidic compounds since they tend to be highly plasma protein bound) but I have used AcOH as an additive with some success.In terms of TLC plates (usually silica on glass in the labs I’ve been in), I have heard that using a high percentage of MeOH is bad, especially for prep TLC, because the MeOH can start to dissolve the binder. I did follow this advice in grad school, and I haven’t had to run prep TLC in my industry job yet J. But I’ve never really done a proper experiment to test this.This conversation could be the basis for a really good paper. You know one of those that people have pinned to their bulletin boards, like Clark Still’s 1978 flash chromatography paper. You make really good points about the quality and size dispersion of the silica as an important factor, and also which solvent the MeOH is paired with. I think that the pore size of the frit that is used is also critical.

Matthew:Hi Jeff, thanks for your thoughts on columns. They are very useful to our group. :)

I've just read Clark Still's 1978 Flash Chromatography. I'd be honoured if our email exchange is pinned below it on the bulletin board.

Jeff:Hi Matt, I’m glad that our discussion helped the group. And I would be honored to have our emails pinned near Clark Still’s paper!